Fake a complete_genomics_pass_all preset.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/vcf2fasta.go b/vcf2fasta.go
index f3faccf4f2b4738e756e6545b2a99dd564878112..eea2f4df303718dcdee39465c4e2096ce3c0b71b 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -285,7 +285,12 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 
                var regions bytes.Buffer
                bedargs := []string{"python2", "-"}
-               if cmd.gvcfType != "" {
+               if cmd.gvcfType == "complete_genomics_pass_all" {
+                       bedargs = append(bedargs,
+                               "--ignore_phrases", "CNV", "INS:ME",
+                               "--unreported_is_called",
+                       )
+               } else if cmd.gvcfType != "" {
                        bedargs = append(bedargs, "--gvcf_type", cmd.gvcfType)
                }
                bedargs = append(bedargs, infile)